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pombase / allele_qc

Quality control for PomBase alleles
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Wrongly labelled gene? #64

Closed manulera closed 1 year ago

manulera commented 1 year ago

Hi @ValWood,

In this paper: https://www.pombase.org/reference/PMID:25720772

The modifications from mug143 do not match the protein sequence. They are likely misanotated because mug143 has never changed gene structure, and it has 121 aminoacids, while in our annotations residue Y343 is mentioned.

I checked if there is a protein that would match all the residues annotated to mug143 that do not match, and I find that dbs2 matches all residues, so likely these protein modification annotations belong to dbs2. Actually, their systematic ids are consecutive: SPAC167.05 for dbs2 and SPAC167.06c for mug143, so I suspect that this was indeed a mistake. If you give me the green light, I will fix those.

systematic_id primary_name modification evidence sequence_position annotation_extension reference taxon date sequence_error
SPAC167.06c mug143 MOD:00046 tryptic phosphop... S107 PMID:25720772 4896 2016-06-27 S107
SPAC167.06c mug143 MOD:00046 tryptic phosphop... S103 PMID:25720772 4896 S103
SPAC167.06c mug143 MOD:00046 tryptic phosphop... S110 PMID:25720772 4896 S110
SPAC167.06c mug143 MOD:00046 tryptic phosphop... S12 PMID:25720772 4896 S12
SPAC167.06c mug143 MOD:00046 tryptic phosphop... S132 PMID:25720772 4896 S132
SPAC167.06c mug143 MOD:00046 tryptic phosphop... S134 PMID:25720772 4896 S134
SPAC167.06c mug143 MOD:00046 tryptic phosphop... S143 PMID:25720772 4896 S143
SPAC167.06c mug143 MOD:00046 tryptic phosphop... S145 PMID:25720772 4896 S145
SPAC167.06c mug143 MOD:00046 tryptic phosphop... S148 PMID:25720772 4896 S148
SPAC167.06c mug143 MOD:00046 tryptic phosphop... S149 PMID:25720772 4896 S149
SPAC167.06c mug143 MOD:00046 tryptic phosphop... S15 PMID:25720772 4896 S15
SPAC167.06c mug143 MOD:00046 tryptic phosphop... S151 PMID:25720772 4896 S151
SPAC167.06c mug143 MOD:00046 tryptic phosphop... S154 PMID:25720772 4896 S154
SPAC167.06c mug143 MOD:00046 tryptic phosphop... S157 PMID:25720772 4896 S157
SPAC167.06c mug143 MOD:00046 tryptic phosphop... S18 PMID:25720772 4896 S18
SPAC167.06c mug143 MOD:00046 tryptic phosphop... S333 PMID:25720772 4896 S333
SPAC167.06c mug143 MOD:00046 tryptic phosphop... S335 PMID:25720772 4896 S335
SPAC167.06c mug143 MOD:00046 tryptic phosphop... S345 PMID:25720772 4896 S345
SPAC167.06c mug143 MOD:00046 tryptic phosphop... S347 PMID:25720772 4896 S347
SPAC167.06c mug143 MOD:00046 tryptic phosphop... S552 PMID:25720772 4896 S552
SPAC167.06c mug143 MOD:00046 tryptic phosphop... S554 PMID:25720772 4896 S554
SPAC167.06c mug143 MOD:00046 tryptic phosphop... S590 PMID:25720772 4896 S590
SPAC167.06c mug143 MOD:00047 tryptic phosphop... T106 PMID:25720772 4896 T106
SPAC167.06c mug143 MOD:00047 tryptic phosphop... T144 PMID:25720772 4896 T144
SPAC167.06c mug143 MOD:00047 tryptic phosphop... T152 PMID:25720772 4896 T152
SPAC167.06c mug143 MOD:00047 tryptic phosphop... T339 PMID:25720772 4896 T339
SPAC167.06c mug143 MOD:00048 tryptic phosphop... Y343 PMID:25720772 4896 Y343
ValWood commented 1 year ago

Yes good catch!

manulera commented 1 year ago

This is now fixed in the svn repository (revision 9037)